Carbobenzyloxy (CBZ) group is commonly used to protect amino and hydroxide groups during organic synthesis. Other similar “carbamate” and “carbonate” protecting groups are also used to protect amino and hydroxyl groups. Chemical deprotection is usually achieved by methods such as hydrogenation with palladium catalyst. However, if other groups are present which are susceptible to the deprotection condition (for example, sulfur during hydrogenation), alternative methods of deprotection are necessary. It would be beneficial to have alternate methods of deprotection that would not destroy susceptible groups. An enzymatic method of deprotection using S. paucimobilis N-carbobenzyloxy-deprotecting enzyme isolated from soil samples has been disclosed in WO 02/053724, which application shares a priority claim with this application. The enzymatic method can be conducted under mild conditions (i.e., aqueous medium at room temp and atmospheric pressure) and without the destroying susceptible groups. Given the importance of the enzyme and its relatively low presence in the host bacterium, it would be useful to clone and express in a heterologous host such as Escherichia coli to ensure a sufficient supply for large-scale reactions.